When used w/ Angel's mods (basically any fluid building w/ multiple inputs/outputs) I see the recipe appearing multiple times for the various permutations in the research tab, e.g., Water Processing 1, but only once for crafting.

This is because the possible permutation recipes are hidden, so they dont clog your recipes. They still need to be activated by the technology, so they appear there.

In the very first releases of GDIW we had all the recipes visible and it was a chaotic hell!!! Then, the idea of hidden the permutations and using hotkeys to change the recipes on the assembler come and was the best change ever for this type of mods!

What nagapito said is true.
This is intended/expected - I generate the permutations and add them to the technologies that unlock the original recipe so that the permutations can be unlocked (only) when the technology is researched.

That said, there might be a way or two around this.
Technically the recipes don't need to be disabled from the start since they are hidden and you cannot access them. But I am not 100% sure of the consequences of this change.
Another approach could be to Not add the permutations to the technologies and enable them via script when you research the technologies.

I will think about it and probably implement the second option.

The first solution, if it has no downsides is way more elegant and clean.
I would ask the devs on the forums if there is some unforseen consequence and if not, implement the 1st.
Less code to maintain and less 'special cases' happening in the game when something is researched.

The thing that worries me is whether you will be able to access the hidden recipes before you research the technology or after technologies are reset and not all of them are researched afterwards.

I am not afraid of more code as long as it doesn't affect performance.

Version 0.0.5 hides the recipes from the Technology screen.